Complexity of Genomic Epidemiology of Carbapenem-Resistant Klebsiella pneumoniae Isolates in Colombia Urges the Reinforcement of Whole Genome Sequencing-Based Surveillance Programs.
Klebsiella pneumoniae
Carbapenemases
antimicrobial resistance
whole genome sequence (WGS)
Journal
Clinical infectious diseases : an official publication of the Infectious Diseases Society of America
ISSN: 1537-6591
Titre abrégé: Clin Infect Dis
Pays: United States
ID NLM: 9203213
Informations de publication
Date de publication:
01 12 2021
01 12 2021
Historique:
entrez:
1
12
2021
pubmed:
2
12
2021
medline:
16
3
2022
Statut:
ppublish
Résumé
Carbapenem-resistant Klebsiella pneumoniae (CRKP) is an emerging public health problem. This study explores the specifics of CRKP epidemiology in Colombia based on whole genome sequencing (WGS) of the National Reference Laboratory at Instituto Nacional de Salud (INS)'s 2013-2017 sample collection. A total of 425 CRKP isolates from 21 departments were analyzed by HiSeq-X10®Illumina high-throughput sequencing. Bioinformatic analysis was performed, primarily using the pipelines developed collaboratively by the National Institute for Health Research Global Health Research Unit (GHRU) on Genomic Surveillance of Antimicrobial Resistance (AMR), and AGROSAVIA. Of the 425 CRKP isolates, 91.5% were carbapenemase-producing strains. The data support a recent expansion and the endemicity of CRKP in Colombia with the circulation of 7 high-risk clones, the most frequent being CG258 (48.39% of isolates). We identified genes encoding carbapenemases blaKPC-3, blaKPC-2, blaNDM-1, blaNDM-9, blaVIM-2, blaVIM-4, and blaVIM-24, and various mobile genetic elements (MGE). The virulence of CRKP isolates was low, but colibactin (clb3) was present in 25.2% of isolates, and a hypervirulent CRKP clone (CG380) was reported for the first time in Colombia. ST258, ST512, and ST4851 were characterized by low levels of diversity in the core genome (ANI > 99.9%). The study outlines complex CRKP epidemiology in Colombia. CG258 expanded clonally and carries specific carbapenemases in specific MGEs, while the other high-risk clones (CG147, CG307, and CG152) present a more diverse complement of carbapenemases. The specifics of the Colombian situation stress the importance of WGS-based surveillance to monitor evolutionary trends of sequence types (STs), MGE, and resistance and virulence genes.
Sections du résumé
BACKGROUND
Carbapenem-resistant Klebsiella pneumoniae (CRKP) is an emerging public health problem. This study explores the specifics of CRKP epidemiology in Colombia based on whole genome sequencing (WGS) of the National Reference Laboratory at Instituto Nacional de Salud (INS)'s 2013-2017 sample collection.
METHODS
A total of 425 CRKP isolates from 21 departments were analyzed by HiSeq-X10®Illumina high-throughput sequencing. Bioinformatic analysis was performed, primarily using the pipelines developed collaboratively by the National Institute for Health Research Global Health Research Unit (GHRU) on Genomic Surveillance of Antimicrobial Resistance (AMR), and AGROSAVIA.
RESULTS
Of the 425 CRKP isolates, 91.5% were carbapenemase-producing strains. The data support a recent expansion and the endemicity of CRKP in Colombia with the circulation of 7 high-risk clones, the most frequent being CG258 (48.39% of isolates). We identified genes encoding carbapenemases blaKPC-3, blaKPC-2, blaNDM-1, blaNDM-9, blaVIM-2, blaVIM-4, and blaVIM-24, and various mobile genetic elements (MGE). The virulence of CRKP isolates was low, but colibactin (clb3) was present in 25.2% of isolates, and a hypervirulent CRKP clone (CG380) was reported for the first time in Colombia. ST258, ST512, and ST4851 were characterized by low levels of diversity in the core genome (ANI > 99.9%).
CONCLUSIONS
The study outlines complex CRKP epidemiology in Colombia. CG258 expanded clonally and carries specific carbapenemases in specific MGEs, while the other high-risk clones (CG147, CG307, and CG152) present a more diverse complement of carbapenemases. The specifics of the Colombian situation stress the importance of WGS-based surveillance to monitor evolutionary trends of sequence types (STs), MGE, and resistance and virulence genes.
Identifiants
pubmed: 34850835
pii: 6447009
doi: 10.1093/cid/ciab777
pmc: PMC8634422
doi:
Substances chimiques
Anti-Bacterial Agents
0
Bacterial Proteins
0
Carbapenems
0
beta-Lactamases
EC 3.5.2.6
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
S290-S299Subventions
Organisme : National Institute for Health Research
ID : 136/111
Investigateurs
Khalil Abudahab
(K)
Harry Harste
(H)
Dawn Muddyman
(D)
Ben Taylor
(B)
Nicole Wheeler
(N)
Sophia David
(S)
Gabriel Beltran
(G)
Felipe Delgadillo
(F)
Erik C D Osma
(ECD)
K L Ravikumar
(KL)
Geetha Nagaraj
(G)
Varun Shamanna
(V)
Vandana Govindan
(V)
Akshata Prabhu
(A)
D Sravani
(D)
M R Shincy
(MR)
Steffimole Rose
(S)
K N Ravishankar
(KN)
Iruka N Okeke
(IN)
Anderson O Oaikhena
(AO)
Ayorinde O Afolayan
(AO)
Jolaade J Ajiboye
(JJ)
Erkison Ewomazino Odih
(E)
Celia Carlos
(C)
Marietta L Lagrada
(ML)
Polle Krystle V Macaranas
(PKV)
Agnettah M Olorosa
(AM)
June M Gayeta
(JM)
Elmer M Herrera
(EM)
Ali Molloy
(A)
John Stelling
(J)
Carolin Vegvari
(C)
Informations de copyright
© The Author(s) 2021. Published by Oxford University Press for the Infectious Diseases Society of America.
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